INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes', e4='PeakXus', fastq='ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF211-rep2-SRR5197079/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.72883701324 s Creating peak regions... Creating peak regions took 66.9116139412 s Estimating background... Estimating background took 64.0309708118 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36210989952 s Creating peak regions... Creating peak regions took 36.170358181 s Estimating background... Estimating background took 27.4092600346 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1451048851 s Creating peak regions... Creating peak regions took 34.8998508453 s Estimating background... Estimating background took 24.8490810394 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-male.chrom.sizes', e4='PeakXus', fastq='ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF211-rep2-SRR5197079/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.09867095947 s Creating peak regions... Creating peak regions took 72.9580180645 s Estimating background... Estimating background took 64.2748038769 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34433698654 s Creating peak regions... Creating peak regions took 36.5024189949 s Estimating background... Estimating background took 27.2676179409 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09518003464 s Creating peak regions... Creating peak regions took 35.6928741932 s Estimating background... Estimating background took 25.6312830448 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25791501999 s Creating peak regions... Creating peak regions took 36.0086939335 s Estimating background... Estimating background took 27.3923990726 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15738487244 s Creating peak regions... Creating peak regions took 31.1513040066 s Estimating background... Estimating background took 28.5576000214 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3583240509 s Creating peak regions... Creating peak regions took 28.0601859093 s Estimating background... Estimating background took 17.0250051022 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06760597229 s Creating peak regions... Creating peak regions took 26.1346950531 s Estimating background... Estimating background took 18.4612898827 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0721218586 s Creating peak regions... Creating peak regions took 23.6001470089 s Estimating background... Estimating background took 17.4864988327 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46524882317 s Creating peak regions... Creating peak regions took 22.7828359604 s Estimating background... Estimating background took 22.6130599976 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79279398918 s Creating peak regions... Creating peak regions took 21.1731860638 s Estimating background... Estimating background took 12.6205239296 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65390992165 s Creating peak regions... Creating peak regions took 17.0301220417 s Estimating background... Estimating background took 14.1102538109 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.37274289131 s Creating peak regions... Creating peak regions took 60.8855268955 s Estimating background... Estimating background took 44.3037240505 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69092488289 s Creating peak regions... Creating peak regions took 18.6681210995 s Estimating background... Estimating background took 14.2933340073 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.983065843582 s Creating peak regions... Creating peak regions took 12.4996278286 s Estimating background... Estimating background took 8.07261586189 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33848977089 s Creating peak regions... Creating peak regions took 14.4683749676 s Estimating background... Estimating background took 13.9392199516 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22756099701 s Creating peak regions... Creating peak regions took 51.8275630474 s Estimating background... Estimating background took 33.7627718449 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8025200367 s Creating peak regions... Creating peak regions took 49.2598631382 s Estimating background... Estimating background took 26.4248929024 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2107129097 s Creating peak regions... Creating peak regions took 47.973965168 s Estimating background... Estimating background took 32.6914041042 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45394802094 s Creating peak regions... Creating peak regions took 45.7819509506 s Estimating background... Estimating background took 37.0980858803 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13120388985 s Creating peak regions... Creating peak regions took 42.946146965 s Estimating background... Estimating background took 32.7210679054 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44471001625 s Creating peak regions... Creating peak regions took 39.1586809158 s Estimating background... Estimating background took 23.3006191254 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89070010185 s Creating peak regions... Creating peak regions took 36.5176329613 s Estimating background... Estimating background took 23.1388192177 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.127146959305 s Creating peak regions... Creating peak regions took 0.215921878815 s Estimating background... Estimating background took 0.665433883667 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08641195297 s Creating peak regions... Creating peak regions took 41.5066580772 s Estimating background... Estimating background took 35.4055538177 s Processing ZNF211-rep2-SRR5197079.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.262468099594 s Creating peak regions... Creating peak regions took 14.2978589535 s Estimating background... Estimating background took 0.71876502037 s